Merge pull request #699 from Steinbeck-Lab/development

fix: segementation download issues

Author: Kohulan

.github/workflows/test.yml

@@ -44,7 +44,7 @@ jobs:
         python -m pip install --upgrade pip
         pip3 install --upgrade setuptools pip
         pip3 install --no-cache-dir -r requirements.txt
-        pip install git+https://github.com/Kohulan/DECIMER-Image-Segmentation.git@bbox --no-deps
+        pip install git+https://github.com/Kohulan/DECIMER-Image-Segmentation.git --no-deps
         pip3 install --no-deps decimer
         pip install flake8 pytest
         pip install pytest-cov

Dockerfile

@@ -31,7 +31,7 @@ RUN conda install -c conda-forge python=${PYTHON_VERSION} sqlite --force-reinsta
     pip3 install --no-cache-dir -r requirements.txt && \
     # Install specific packages without dependencies
     pip3 install --no-cache-dir --no-deps \
-        git+https://github.com/Kohulan/DECIMER-Image-Segmentation.git@bbox \
+        git+https://github.com/Kohulan/DECIMER-Image-Segmentation.git \
         decimer==2.7.1 \
         chembl_structure_pipeline
 

requirements.txt

@@ -34,3 +34,4 @@ openbabel-wheel
 uvicorn[standard]
 pytest
 pytest-asyncio
+pymupdf